Antibiotic-treated versus germ-free rodents for microbiota transplantation studies

References

• Kirk RG. “Life in a germ-free world:” isolating life from the laboratory animal to the bubble boy. Bull Hist Med 2012; 86:237-75; PMID:23000838; http://dx.doi.org/10.1353/bhm.2012.0028
   PubMed Web of Science ®Google Scholar
• Hansen AK, Nielsen DS. Handbook of Laboratory Animal Bacteriology, Second Edition - CRC Press Book. 2nd ed. CRC Press; 2014
   Google Scholar
• Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006; 444:1027-31; PMID:17183312; http://dx.doi.org/10.1038/nature05414
   PubMed Web of Science ®Google Scholar
• Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, Deng Y, Blennerhassett P, Macri J, McCoy KD, et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 2011; 141:599-609, 609.e1-3; http://dx.doi.org/10.1053/j.gastro.2011.04.052
   PubMed Web of Science ®Google Scholar
• Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008; 455:1109-13; PMID:18806780; http://dx.doi.org/10.1038/nature07336
   PubMed Web of Science ®Google Scholar
• Bäckhed F, Ding H, Wang T, Hooper L V, Koh GY, Nagy A, Semenkovich CF, Gordon JI. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 2004; 101:15718-23; http://dx.doi.org/10.1073/pnas.0407076101
   PubMed Web of Science ®Google Scholar
• Hansen CHF, Nielsen DS, Kverka M, Zakostelska Z, Klimesova K, Hudcovic T, Tlaskalova-Hogenova H, Hansen AK. Patterns of early gut colonization shape future immune responses of the host. PLoS One 2012; 7:e34043; PMID:22479515; http://dx.doi.org/10.1371/journal.pone.0034043
   PubMed Web of Science ®Google Scholar
• Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005; 122:107-18; PMID:16009137; http://dx.doi.org/10.1016/j.cell.2005.05.007
   PubMed Web of Science ®Google Scholar
• Neufeld K-AM, Kang N, Bienenstock J, Foster JA. Effects of intestinal microbiota on anxiety-like behavior. Commun Integr Biol 2011; 4:492-4; PMID:21966581; http://dx.doi.org/10.4161/cib.15702
   PubMedGoogle Scholar
• Olszak T, An D, Zeissig S, Vera MP, Richter J, Franke A, Glickman JN, Siebert R, Baron RM, Kasper DL, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 2012; 336:489-93; PMID:22442383; http://dx.doi.org/10.1126/science.1219328
   PubMed Web of Science ®Google Scholar
• Schéle E, Grahnemo L, Anesten F, Hallén A, Bäckhed F, Jansson JO. The gut microbiota reduces leptin sensitivity and the expression of the obesity-suppressing neuropeptides proglucagon (Gcg) and brain-derived neurotrophic factor (Bdnf) in the central nervous system. Endocrinology 2013; 154:3643-51; http://dx.doi.org/10.1210/en.2012-2151
   PubMed Web of Science ®Google Scholar
• Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y. Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. J Physiol 2004; 558:263-75; PMID:15133062; http://dx.doi.org/10.1113/jphysiol.2004.063388
   PubMed Web of Science ®Google Scholar
• Bleich A, Mahler M. Environment as a critical factor for the pathogenesis and outcome of gastrointestinal disease: experimental and human inflammatory bowel disease and helicobacter-induced gastritis. Pathobiology 2005; 72:293-307; PMID:16582581; http://dx.doi.org/10.1159/000091327
   PubMed Web of Science ®Google Scholar
• Sellon RK, Tonkonogy S, Schultz M, Dieleman LA, Grenther W, Balish E, Rennick DM, Sartor RB. Resident enteric bacteria are necessary for development of spontaneous colitis and immune system activation in interleukin-10-deficient mice. Infect Immun 1998; 66:5224-31; PMID:9784526
   PubMed Web of Science ®Google Scholar
• Song F, Ito K, Denning TL, Kuninger D, Papaconstantinou J, Gourley W, Klimpel G, Balish E, Hokanson J, Ernst PB. Expression of the neutrophil chemokine KC in the colon of mice with enterocolitis and by intestinal epithelial cell lines: effects of flora and proinflammatory cytokines. J Immunol 1999; 162:2275-80; PMID:9973504
   PubMed Web of Science ®Google Scholar
• Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012; 490:55-60; PMID:23023125; http://dx.doi.org/10.1038/nature11450
   PubMed Web of Science ®Google Scholar
• Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 2010; 156:3205-15; PMID:20705664; http://dx.doi.org/10.1099/mic.0.043257-0
   PubMed Web of Science ®Google Scholar
• Ellekilde M, Selfjord E, Larsen CS, Jakesevic M, Rune I, Tranberg B, Vogensen FK, Nielsen DS, Bahl MI, Licht TR, et al. Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice. Sci Rep 2014; 4:5922; PMID:25082483; http://dx.doi.org/10.1038/srep05922
   PubMed Web of Science ®Google Scholar
• Paik J, Pershutkina O, Meeker S, Yi JJ, Dowling S, Hsu C, Hajjar AM, Maggio-Price L, Beck DAC. Potential for using a hermetically-sealed, positive-pressured isocage system for studies involving germ-free mice outside a flexible-film isolator. Gut Microbes 2015; 6:255-65; PMID:26177210; http://dx.doi.org/10.1080/19490976.2015.1064576
   PubMed Web of Science ®Google Scholar
• Hansen AK. Antibiotic treatment of nude rats and its impact on the aerobic bacterial flora. Lab Anim 1995; 29:37-44; PMID:7707676; http://dx.doi.org/10.1258/002367795780740410
   PubMed Web of Science ®Google Scholar
• Candon S, Perez-Arroyo A, Marquet C, Valette F, Foray AP, Pelletier B, Milani C, Ventura M, Bach JF, Chatenoud L. Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes. PLoS One 2015; 10:e0125448; PMID:25970503; http://dx.doi.org/10.1371/journal.pone.0125448
   PubMed Web of Science ®Google Scholar
• Hansen CHF, Krych L, Nielsen DS, Vogensen FK, Hansen LH, Sørensen SJ, Buschard K, Hansen AK. Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse. Diabetologia 2012; 55:2285-94; PMID:22572803; http://dx.doi.org/10.1007/s00125-012-2564-7
   PubMed Web of Science ®Google Scholar
• Weng M, Walker WA. The role of gut microbiota in programming the immune phenotype. J Dev Orig Health Dis 2013; 4:203-14; PMID:24353893; http://dx.doi.org/10.1017/S2040174412000712
   PubMed Web of Science ®Google Scholar
• Barfod KK, Roggenbuck M, Hansen LH, Schjørring S, Larsen ST, Sørensen SJ, Krogfelt KA. The murine lung microbiome in relation to the intestinal and vaginal bacterial communities. BMC Microbiol 2013; 13:303; PMID:24373613; http://dx.doi.org/10.1186/1471-2180-13-303
   PubMed Web of Science ®Google Scholar
• Srinivas G, Möller S, Wang J, Künzel S, Zillikens D, Baines JF, Ibrahim SM. Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering. Nat Commun 2013; 4:2462; PMID:24042968; http://dx.doi.org/10.1038/ncomms3462
   PubMed Web of Science ®Google Scholar
• Underhill DM, Iliev ID. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol 2014; 14:405-16; PMID:24854590; http://dx.doi.org/10.1038/nri3684
   PubMed Web of Science ®Google Scholar
• Virgin HW. The virome in mammalian physiology and disease. Cell 2014; 157:142-50; PMID:24679532; http://dx.doi.org/10.1016/j.cell.2014.02.032
   PubMed Web of Science ®Google Scholar
• Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, et al. Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences. Cell 2014; 158:705-21; PMID:25126780; http://dx.doi.org/10.1016/j.cell.2014.05.052
   PubMed Web of Science ®Google Scholar
• Han D, Walsh MC, Kim KS, Hong SW, Lee J, Yi J, Rivas G, Surh CD, Choi Y. Microbiota-independent ameliorative effects of antibiotics on spontaneous th2-associated pathology of the small intestine. PLoS One 2015; 10:e0118795; PMID:25689829; http://dx.doi.org/10.1371/journal.pone.0118795
   PubMedGoogle Scholar
• Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 2015; 64:1732-43; PMID:25614621; http://dx.doi.org/10.1136/gutjnl-2014-308820
   PubMed Web of Science ®Google Scholar
• Modi SR, Lee HH, Spina CS, Collins JJ. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 2013; 499:219-22; PMID:23748443; http://dx.doi.org/10.1038/nature12212
   PubMed Web of Science ®Google Scholar
• Bleich A, Hansen AK. Time to include the gut microbiota in the hygienic standardisation of laboratory rodents. Comp Immunol Microbiol Infect Dis 2012; 35:81-92; PMID:22257867; http://dx.doi.org/10.1016/j.cimid.2011.12.006
   PubMed Web of Science ®Google Scholar
• Hansen AK, Friis Hansen CH, Krych L, Nielsen DS. Impact of the gut microbiota on rodent models of human disease. World J Gastroenterol 2014; 20:17727-36; PMID:25548471
   PubMed Web of Science ®Google Scholar
• Macpherson AJ, McCoy KD. Standardised animal models of host microbial mutualism. Mucosal Immunol 2015; 8:476-86; PMID:25492472; http://dx.doi.org/10.1038/mi.2014.113
   PubMed Web of Science ®Google Scholar
• Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, et al. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012; 488:621-6; PMID:22914093; http://dx.doi.org/10.1038/nature11400
   PubMed Web of Science ®Google Scholar
• Desbonnet L, Clarke G, Traplin A, O'sullivan O, Crispie F, Moloney RD, Cotter PD, Dinan TG, Cryan JF. Gut Microbiota Depletion from Early Adolescence in Mice: Implications for Brain and Behaviour. Brain Behav Immun 2015; 50:335-6
   PubMed Web of Science ®Google Scholar
• Rune I, Hansen CHF, Ellekilde M, Nielsen DS, Skovgaard K, Rolin BC, Lykkesfeldt J, Josefsen K, Tranberg B, Kihl P, et al. Ampicillin-improved glucose tolerance in diet-induced obese C57BL/6NTac mice is age dependent. J Diabetes Res 2013; 2013:319321; PMID:24369539; http://dx.doi.org/10.1155/2013/319321
   PubMed Web of Science ®Google Scholar
• Alam C, Bittoun E, Bhagwat D, Valkonen S, Saari A, Jaakkola U, Eerola E, Huovinen P, Hänninen A. Effects of a germ-free environment on gut immune regulation and diabetes progression in non-obese diabetic (NOD) mice. Diabetologia 2011; 54:1398-406; PMID:21380595; http://dx.doi.org/10.1007/s00125-011-2097-5
   PubMed Web of Science ®Google Scholar
• Greiner TU, Hyötyläinen T, Knip M, Bäckhed F, Orešič M. The gut microbiota modulates glycaemic control and serum metabolite profiles in non-obese diabetic mice. PLoS One 2014; 9:e110359; PMID:25390735; http://dx.doi.org/10.1371/journal.pone.0110359
   PubMedGoogle Scholar
• Braniste V, Al-Asmakh M, Kowal C, Anuar F, Abbaspour A, Toth M, Korecka A, Bakocevic N, Guan NL, Kundu P, et al. The gut microbiota influences blood-brain barrier permeability in mice. Sci Transl Med 2014; 6:263ra158-263ra158; PMID:25411471; http://dx.doi.org/10.1126/scitranslmed.3009759
   PubMed Web of Science ®Google Scholar
• Heijtz RD, Wang S, Anuar F, Qian Y, Bjorkholm B, Samuelsson A, Hibberd ML, Forssberg H, Pettersson S. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci 2011; 108:3047-52; PMID:21282636; http://dx.doi.org/10.1073/pnas.1010529108
   PubMed Web of Science ®Google Scholar
• Smith K, McCoy KD, Macpherson AJ. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 2007; 19:59-69; PMID:17118672; http://dx.doi.org/10.1016/j.smim.2006.10.002
   PubMed Web of Science ®Google Scholar
• Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F. Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res 2010; 20:1411-9; PMID:20736229; http://dx.doi.org/10.1101/gr.107987.110
   PubMed Web of Science ®Google Scholar
• Hu Y, Peng J, Tai N, Hu C, Zhang X, Wong FS, Wen L. Maternal Antibiotic Treatment Protects Offspring from Diabetes Development in Nonobese Diabetic Mice by Generation of Tolerogenic APCs. J Immunol 2015; 195:4176-84; PMID:26401004; http://dx.doi.org/10.4049/jimmunol.1500884
   PubMed Web of Science ®Google Scholar
• Peng J, Narasimhan S, Marchesi JR, Benson A, Wong FS, Wen L. Long term effect of gut microbiota transfer on diabetes development. J Autoimmun 2014; 53:85-94; PMID:24767831; http://dx.doi.org/10.1016/j.jaut.2014.03.005
   PubMed Web of Science ®Google Scholar
• Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013; 341:1241214; PMID:24009397; http://dx.doi.org/10.1126/science.1241214
   PubMed Web of Science ®Google Scholar
• Celaj S, Gleeson MW, Deng J, O'Toole GA, Hampton TH, Toft MF, Morrison HG, Sogin ML, Putra J, Suriawinata AA, et al. The microbiota regulates susceptibility to Fas-mediated acute hepatic injury. Lab Invest 2014; 94:938-49; PMID:25068658; http://dx.doi.org/10.1038/labinvest.2014.93
   PubMed Web of Science ®Google Scholar
• Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV. Gender bias in autoimmunity is influenced by microbiota. Immunity 2013; 39:400-12; PMID:23973225; http://dx.doi.org/10.1016/j.immuni.2013.08.013
   PubMed Web of Science ®Google Scholar
• Hansen CHF, Andersen LSF, Krych L, Metzdorff SB, Hasselby JP, Skov S, Nielsen DS, Buschard K, Hansen LH, Hansen AK. Mode of delivery shapes gut colonization pattern and modulates regulatory immunity in mice. J Immunol 2014; 193:1213-22; PMID:24951818; http://dx.doi.org/10.4049/jimmunol.1400085
   PubMed Web of Science ®Google Scholar
• Daft JG, Ptacek T, Kumar R, Morrow C, Lorenz RG. Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother. Microbiome 2015; 3:17; PMID:25969735; http://dx.doi.org/10.1186/s40168-015-0080-y
   PubMed Web of Science ®Google Scholar